Cross-reference for Gene expression (GenEx) ontology classes, object properties and data properties back to ToC

This section provides details for each class and property defined by Gene expression (GenEx) ontology.

Classes

absence of gene expressionc back to ToC or Class ToC

IRI: http://purl.org/genex#AbsenceExpression

Example
@prefix bgee: <http://bgee.org/#> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
@prefix orth: <http://purl.org/net/orth#> .
@prefix genex: <http://purl.org/genex#> .

bgee:NOT_EXPRESSED_310632766 rdf:type genex:AbsenceExpression ;
    genex:hasExpressionLevel 6.44034 ;
    genex:hasConfidenceLevel obo:CIO_0000029 ;
    genex:hasFDRpvalue 1.0 ;
    genex:hasSequenceUnit oma:ENSXETG00000010593 ;
    genex:hasExpressionCondition bgee:EXPRESSION_CONDITION_134065 . 
has super-classes
is in domain of
has an expression condition op, has expression level score dp, has expression or absence confidence level op, has false discovery rate p-value dp, has sequence unit op

anatomical entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CARO_0000000

A part of a multicellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a multicellular organism with granularity above the level of a protein complex.
Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.
has super-classes
Anatomical entity c

Anatomical entityc back to ToC or Class ToC

IRI: http://purl.org/genex#AnatomicalEntity

An anatomical entity can be an organism part (e.g. brain, blood, liver and so on) or a material anatomical entity such as a cell.
Example
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .

obo:UBERON_0000310 rdf:type genex:AnatomicalEntity ;
    dcterms:description "The upper ventral region of the torso of an organism." ;
    rdfs:label "breast" .  
has super-classes
biological entity c
has sub-classes
anatomical entity c, organism part c
is in range of
has anatomical entity op, is absent in op, is expressed in op

biological entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CARO_0030000

Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.
Important for alignment with Darwin Core class "Organism".
has super-classes
independent continuant c
has sub-classes
Anatomical entity c

Cluster of homologous sequencesc back to ToC or Class ToC

IRI: http://purl.org/net/orth#HomologsCluster

Set of homologous sequences
is in range of
see also OMA group ap

continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000002

Is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
entity c
has sub-classes
independent continuant c
is in domain of
expressed in op, genomically related to op
is in range of
genomically related to op

databasec back to ToC or Class ToC

IRI: http://semanticscience.org/resource/SIO_000750

A database is a data store such as relational, hierarchical and graph databases.

developmental stagec back to ToC or Class ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0000399

A developmental stage is spatiotemporal region encompassing some part of the life cycle of an organism, e.g. blastula stage
This branch will be replaced by, and if necessary merged with an Uberon import in future.
Example
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .

obo:BtauDv_0000007 rdf:type efo:EFO_0000399 ;
    dcterms:description "Embryo development period during the first 3 months of gestation, up to day 90 of development." ;
    rdfs:label "first trimester of gestation (cow)". 
has super-classes
process c
is in range of
has a developmental stage op, is absent in op, is expressed in op

entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000001

Is defined by
http://purl.obolibrary.org/obo/bfo.owl
has sub-classes
continuant c

experimental factorc back to ToC or Class ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0000001

An experimental factor in Array Express which are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This upper level class is really used to give a root class from which applications can rely on and not be tied to upper ontology classses which do change.
Concept naming convention is lower case natural naming with spaces, when necessary captials should be used, for example disease factor, HIV, breast carcinoma, Ewing's sarcoma
has sub-classes
material entity c, process c
is disjoint with
Obsolete Class c

Genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000704

Is defined by
http://www.ontobee.org/ontology/SO?iri=http://purl.obolibrary.org/obo/SO_0000704
is equivalent to
Gene c
is in range of
see also Ensembl gene ap

Genec back to ToC or Class ToC

IRI: http://purl.org/net/orth#Gene

Is defined by
https://github.com/qfo/OrthologyOntology
Example
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
@prefix orth: <http://purl.org/net/orth#> .
@prefix lscr: <http://purl.org/lscr#> .
@prefix up-data: <http://purl.uniprot.org/uniprot/> .

oma:ENSG00000130208 rdf:type orth:Gene ;
    dcterms:description "apolipoprotein C1 [Source:HGNC Symbol;Acc:HGNC:607]" ;
    rdfs:label "first trimester of gestation (cow)";
    dcterms:identifier "ENSG00000130208" ;
    rdfs:seeAlso <https://www.bgee.org/bgee15_1/gene/ENSG00000130208> ;
    lscr:xrefUniprot  up-data:P02654 ; 
    lscr:xrefEnsemblGene  <http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000130208> . 
has super-classes
Sequence unit c

gene expressionc back to ToC or Class ToC

IRI: http://purl.org/genex#Expression

All sequence units (e.g. Gene) that are expressed in some condition (e.g. organ and/or adult stage).
Example
@prefix bgee: <http://bgee.org/#> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
@prefix orth: <http://purl.org/net/orth#> .
@prefix genex: <http://purl.org/genex#> .

bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
    genex:hasExpressionLevel 83.9292 ;
    genex:hasConfidenceLevel obo:CIO_0000029 ;
    genex:hasFDRpvalue 0.00188199 ;
    genex:hasSequenceUnit oma:ENSMUSG00000022751 ;
    genex:hasExpressionCondition bgee:EXPRESSION_CONDITION_354899 . 
has super-classes
is in domain of
has an expression condition op, has expression level characteristic op, has expression level score dp, has expression or absence confidence level op, has false discovery rate p-value dp, has sequence unit op

gene expression experiment conditionc back to ToC or Class ToC

IRI: http://purl.org/genex#ExpressionCondition

A sequence unit (e.g. Gene) is expressed in some expression condition (e.g. anatomical entity and/or developmental stage).
Example
@prefix bgee: <http://bgee.org/#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .

bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ;
  genex:hasSex "any";
  genex:hasStrain bgee:STRAIN_3d4eba69908860b0d838be983fd7f9c8 ;
  genex:hasAnatomicalEntity obo:UBERON_0000080 ;
  genex:hasDevelopmentalStage obo:UBERON_0000113  . 
is equivalent to
(has anatomical entity op some Anatomical entity c) or (has a developmental stage op some developmental stage c) or (has strain op some strain c) or (has Sex dp some string)
has super-classes
is in domain of
has Sex dp, has a developmental stage op, has anatomical entity op, has strain op
is in range of
has an expression condition op, is absent in op, is expressed in op

gene regionc back to ToC or Class ToC

IRI: http://purl.org/net/orth#Subgene

A region of the sequence of the gene
has super-classes
Sequence unit c

Gene tree nodec back to ToC or Class ToC

IRI: http://purl.org/net/orth#GeneTreeNode

A node of a tree whose leaf nodes are sequence units and whose internal nodes are clusters of homologs
has super-classes
Node c
has sub-classes
Sequence unit c

independent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000004

b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
Is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
has super-classes
continuant c
has sub-classes
biological entity c
is in range of
expressed in op

material entityc back to ToC or Class ToC

IRI: http://www.ifomis.org/bfo/1.1/snap#MaterialEntity

A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray.
Example
A heart, a human, a fly, a microarray.
has super-classes
experimental factor c
has sub-classes
organism part c

Nodec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000140

Basic unit of graphs and trees
has sub-classes
Gene tree node c

Organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C14250

is equivalent to
Organism c

Organismc back to ToC or Class ToC

IRI: http://purl.org/net/orth#Organism

A living being, such as an animal, a plant, a bacterium, or a fungus., Any individual living (or previously living) being. Example: animal, human being. An organim can be associated to a taxon such as "Homo Sapiens", NCBI taxonomy identifier: 9606.
has super-classes
is in range of
organism op

organism partc back to ToC or Class ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0000635

The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).
Example
tissue, organ, system, sperm, blood or body location (arm).
has super-classes
Anatomical entity c, material entity c

polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000104

is equivalent to
Protein c

populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000181

A population is a group of material entities consisting of individuals which share a particular characteristic such as inhabiting a particular region or area or ability to interbreed.
has sub-classes
strain c

processc back to ToC or Class ToC

IRI: http://www.ifomis.org/bfo/1.1/span#ProcessualEntity

A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs.
has super-classes
experimental factor c
has sub-classes
developmental stage c

Proteinc back to ToC or Class ToC

IRI: http://purl.org/net/orth#Protein

Is defined by
https://github.com/qfo/OrthologyOntology
has super-classes
Sequence unit c
is in range of
see also OMA protein ap

Proteinc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Protein

Is defined by
http://purl.uniprot.org/core/
is in range of
see also UniProt cross-reference ap, see also UniProt/SwissProt cross-reference ap, see also UniProt/TrEMBL cross-reference ap

proteinc back to ToC or Class ToC

IRI: http://rdf.ebi.ac.uk/terms/ensembl/protein

Is defined by
https://www.ebi.ac.uk/rdf/documentation/ensembl/
is in range of
see also Ensembl protein ap

Sequence unitc back to ToC or Class ToC

IRI: http://purl.org/net/orth#SequenceUnit

protein or DNA sequence as a unit of comparison
has super-classes
Gene tree node c
has sub-classes
Gene c, Protein c, gene region c
is in domain of
is absent in op, is expressed in op, organism op
is in range of
has sequence unit op

strainc back to ToC or Class ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0005135

A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics.
has super-classes
population c
is in range of
has strain op, is absent in op, is expressed in op

Taxonc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Taxon

An element of a taxonomy for classifying life forms.
Example
@prefix up: <http://purl.uniprot.org/core/> .
@prefix up-taxon: <http://purl.uniprot.org/taxonomy/> .
up-taxon:10090 rdf:type up:Taxon ;
    up:rank up:Species . 
has super-classes
is in domain of
rank op, replaces op
is in range of
replaces op

Taxon rankc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Rank

A rank of a taxon.
is in range of
rank op
has members
Taxonomic rank Species ni

Transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000673

Is defined by
https://www.ebi.ac.uk/rdf/documentation/ensembl/
is in range of
see also Ensembl transcript ap

Object Properties

contained inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001018

encodesop back to ToC or Object Property ToC

IRI: http://semanticscience.org/resource/SIO_010078

expressed inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002206

x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
Example
'neural crest cell'  SubClassOf expresses some 'Wnt1 gene'
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .

obo:UBERON_0000310 rdf:type genex:AnatomicalEntity .
oma:ENSMUSG00000002396 rdf:type orth:Gene ;
    obo:RO_0002206 obo:UBERON_0000310 .
has super-properties
genomically related to op
has sub-properties
is expressed in op
has domain
continuant c
has range
independent continuant c
is inverse of
expresses op

expressesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002292

Inverse of 'expressed in'
Example
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .

obo:UBERON_0000310 rdf:type genex:AnatomicalEntity ;
    obo:RO_0002292 oma:ENSMUSG00000002396 .
oma:ENSMUSG00000002396 rdf:type orth:Gene .  
has super-properties
genomically related to op
has sub-properties
ubiquitously expresses op
is inverse of
expressed in op

genomically related toop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002330

holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
has sub-properties
expressed in op, expresses op, is absent in op
has domain
continuant c
has range
continuant c

has a developmental stageop back to ToC or Object Property ToC

IRI: http://purl.org/genex#hasDevelopmentalStage

Example
@prefix bgee: <http://bgee.org/#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .

bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ;
  genex:hasDevelopmentalStage obo:UBERON_0000113 .
obo:UBERON_0000113  rdf:type efo:EFO_0000399 . 

has characteristics: functional

has domain
gene expression experiment condition c
has range
developmental stage c

has an expression conditionop back to ToC or Object Property ToC

IRI: http://purl.org/genex#hasExpressionCondition

Example
@prefix bgee: <http://bgee.org/#> .
@prefix orth: <http://purl.org/net/orth#> .
@prefix genex: <http://purl.org/genex#> .

bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
    genex:hasExpressionCondition bgee:EXPRESSION_CONDITION_354899 . 
bgee:EXPRESSION_CONDITION_354899 rdf:type genex:ExpressionCondition . 

has anatomical entityop back to ToC or Object Property ToC

IRI: http://purl.org/genex#hasAnatomicalEntity

Example
@prefix bgee: <http://bgee.org/#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .

bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ;
  genex:hasAnatomicalEntity obo:UBERON_0000080 .
obo:UBERON_0000080  rdf:type genex:AnatomicalEntity. 

has characteristics: functional

has domain
gene expression experiment condition c
has range
Anatomical entity c

has expression level characteristicop back to ToC or Object Property ToC

IRI: http://purl.org/genex#hasExpressionCharacteristic

Example
@prefix bgee: <http://bgee.org/#> .
@prefix genex: <http://purl.org/genex#> .

bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
    genex:hasExpressionCharacteristic  genex:AVERAGE_EXPRESSED . 

has characteristics: functional

has domain
gene expression c
has range
{ average expressed ni , highly expressed ni , high expressed ni , lowly expressed ni , low expressed ni , ubiquitously expressed ni }

has expression or absence confidence levelop back to ToC or Object Property ToC

IRI: http://purl.org/genex#hasConfidenceLevel

Example
@prefix bgee: <http://bgee.org/#> .
@prefix genex: <http://purl.org/genex#> .

bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
    genex:hasConfidenceLevel obo:CIO_0000029 . 

has characteristics: functional

has domain
absence of gene expression c or gene expression c
has range
{ high confidence level ni , medium confidence level ni , low confidence level ni }

has sequence unitop back to ToC or Object Property ToC

IRI: http://purl.org/genex#hasSequenceUnit

Example
@prefix bgee: <http://bgee.org/#> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
@prefix orth: <http://purl.org/net/orth#> .
@prefix genex: <http://purl.org/genex#> .

bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
    genex:hasSequenceUnit oma:ENSMUSG00000022751 .
oma:ENSMUSG00000022751 a orth:Gene . 

has strainop back to ToC or Object Property ToC

IRI: http://purl.org/genex#hasStrain

Example
@prefix bgee: <http://bgee.org/#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .

bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ;
  genex:hasStrain bgee:STRAIN_3d4eba69908860b0d838be983fd7f9c8 .
bgee:STRAIN_3d4eba69908860b0d838be983fd7f9c8  rdf:type efo:EFO_0005135  ;
    rdfs:label "wild-type" 

has characteristics: functional

has domain
gene expression experiment condition c
has range
strain c

in taxonop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002162

Connects a biological entity to its taxon of origin.
Example
@prefix bgee-species: <https://bgee.org/species/> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix up-taxon: <http://purl.uniprot.org/taxonomy/> .

bgee-species:10090 rdf:type orth:Organism ;
    obo:RO_0002162  up-taxon:10090  .
up-taxon:10090 rdf:type up:Taxon ;
    up:scientificName "Mus musculus". 

is absent inop back to ToC or Object Property ToC

IRI: http://purl.org/genex#isAbsentIn

A sequence unit is absent (not expressed) in some expression condition (e.g. anatomical entity and/or developmental stage). Examples how to assign this property (at a high level of abstraction): GeneA "is absent in" Brain; GeneA "is abent in" adult stage.

is expressed inop back to ToC or Object Property ToC

IRI: http://purl.org/genex#isExpressedIn

A sequence unit (e.g. gene) is present (expressed) in some expression condition (e.g. anatomical entity and/or developmental stage). Examples how to assign this property (at a high level of abstraction): GeneA "is expressed in" Brain; GeneA "is expressed in" adult stage.
Example
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .

obo:UBERON_0000310 rdf:type genex:AnatomicalEntity .
oma:ENSMUSG00000002396 rdf:type orth:Gene ;
    genex:isExpressedIn obo:UBERON_0000310 .

organismop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#organism

Example
@prefix bgee-species: <https://bgee.org/species/> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .

oma:ENSMUSG00000002396 rdf:type orth:Gene ;
    orth:organism  bgee-species:10090 .
has domain
Sequence unit c
has range
Organism c

over-expressed inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002245

g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.
has super-properties
is expressed in op

part_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000194

rankop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/rank

The rank of a taxon.

has characteristics: functional

has domain
Taxon c
has range
Taxon rank c

replacesop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/replaces

A resource that is replaced by this resource.
has domain
Taxon c
has range
Taxon c

ubiquitously expressed inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002291

x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
has super-properties
is expressed in op
is inverse of
ubiquitously expresses op

ubiquitously expressesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002293

inverse of ubiquiotously expressed in
has super-properties
expresses op
is inverse of
ubiquitously expressed in op

under-expressed inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002246

g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.
has super-properties
is expressed in op

Data Properties

common namedp back to ToC or Data Property ToC

IRI: http://purl.uniprot.org/core/commonName

Is defined by
http://purl.uniprot.org/core/
Example
@prefix up: <http://purl.uniprot.org/core/> .
@prefix up-taxon: <http://purl.uniprot.org/taxonomy/> .
up-taxon:10090 rdf:type up:Taxon ;
    up:commonName "mouse" . 

has characteristics: functional

has range
string

Descriptiondp back to ToC or Data Property ToC

IRI: http://purl.org/dc/elements/1.1/description

An account of the resource.
Is defined by
http://purl.org/dc/elements/1.1/
has range
Literal

has expression level scoredp back to ToC or Data Property ToC

IRI: http://purl.org/genex#hasExpressionLevel

Example
@prefix bgee: <http://bgee.org/#> .
@prefix genex: <http://purl.org/genex#> .

bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
    genex:hasExpressionLevel 83.9292 . 
has domain
absence of gene expression c or gene expression c
has range
double

has false discovery rate p-valuedp back to ToC or Data Property ToC

IRI: http://purl.org/genex#hasFDRpvalue

Example
@prefix bgee: <http://bgee.org/#> .
@prefix genex: <http://purl.org/genex#> .

bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
    genex:hasFDRpvalue 0.00188199 . 
has domain
absence of gene expression c or gene expression c
has range
double

has Sexdp back to ToC or Data Property ToC

IRI: http://purl.org/genex#hasSex

Example
@prefix bgee: <http://bgee.org/#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .

bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ;
  genex:hasSex "any" . 

has characteristics: functional

has domain
gene expression experiment condition c
has range
{ "NA" , "any" , "female" , "hermaphrodite" , "male" , "mixed" , "not annotated" }

Identifierdp back to ToC or Data Property ToC

IRI: http://purl.org/dc/terms/identifier

An unambiguous reference to the resource within a given context.
Is defined by
http://purl.org/dc/terms/
has range
Literal

Mnemonicdp back to ToC or Data Property ToC

IRI: http://purl.uniprot.org/core/mnemonic

A easy to remember identifier for a UniProtKB entry, but it is not a stable identifier and should not be used by programs to identify entries.
has range
string

scientific namedp back to ToC or Data Property ToC

IRI: http://purl.uniprot.org/core/scientificName

Is defined by
http://purl.uniprot.org/core/
Example
@prefix up: <http://purl.uniprot.org/core/> .
@prefix up-taxon: <http://purl.uniprot.org/taxonomy/> .
up-taxon:10090 rdf:type up:Taxon ;
    up:scientificName "Mus musculus". 

has characteristics: functional

has range
string

Annotation Properties

abstractap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/abstract

alternative labelap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#altLabel

The range of skos:altLabel is the class of RDF plain literals.
An alternative lexical label for a resource.
Is defined by
http://www.w3.org/2004/02/skos/core
Example
Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel).
has super-properties
label

alternative_termap back to ToC or Annotation Property ToC

IRI: http://www.ebi.ac.uk/efo/alternative_term

An alternative label for a given entity such as a commonly used abbreviation or synonym.

bibliographic Citationap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/bibliographicCitation

change Noteap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#changeNote

code Repositoryap back to ToC or Annotation Property ToC

IRI: http://schema.org/codeRepository

contributorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/contributor

createdap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/created

creatorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/creator

curator noteap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000232

Is defined by
http://purl.obolibrary.org/obo/iao.owl

definitionap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000115

definitionap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#definition

A statement or formal explanation of the meaning of a concept.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
note ap

definition citationap back to ToC or Annotation Property ToC

IRI: http://www.ebi.ac.uk/efo/definition_citation

A definition citation is a document, ontology class, person or organization from which the definition of the class is derived. It is used in the same sense as a citation in literature, in that the definition may have been derived from these sources or that this definition is related to these source.
has sub-properties
N C I Thesaurus definition citation ap

Descriptionap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/description

editor noteap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000116

Is defined by
http://purl.obolibrary.org/obo/iao.owl

elucidationap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000600

Is defined by
http://purl.obolibrary.org/obo/iao.owl

exampleap back to ToC or Annotation Property ToC

IRI: http://purl.org/vocab/vann/example

exampleap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#example

An example of the use of a concept.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
note ap

example of usageap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000112

extendsap back to ToC or Annotation Property ToC

IRI: http://purl.org/vocommons/voaf#extends

homepageap back to ToC or Annotation Property ToC

IRI: http://xmlns.com/foaf/0.1/homepage

idap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#id

imageap back to ToC or Annotation Property ToC

IRI: http://schema.org/image

in databaseap back to ToC or Annotation Property ToC

IRI: http://purl.org/net/orth#inDatabase

A property to define the database an orthology dataset belongs to.
has domain
Orthology Dataset ep

in Subsetap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#inSubset

introductionap back to ToC or Annotation Property ToC

IRI: https://w3id.org/widoco/vocab#introduction

issueap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/issue

licenseap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/license

member Ofap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/ns/org#memberOf

modifiedap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/modified

N C I Thesaurus definition citationap back to ToC or Annotation Property ToC

IRI: http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation

http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation is an annotation property that is drawn from NCI_Thesaurus
has super-properties
definition citation ap

nameap back to ToC or Annotation Property ToC

IRI: http://xmlns.com/foaf/0.1/name

noteap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#note

A general note, for any purpose.
Is defined by
http://www.w3.org/2004/02/skos/core
has sub-properties
definition ap, example ap, scope note ap

preferred Namespace Prefixap back to ToC or Annotation Property ToC

IRI: http://purl.org/vocab/vann/preferredNamespacePrefix

preferred Namespace Uriap back to ToC or Annotation Property ToC

IRI: http://purl.org/vocab/vann/preferredNamespaceUri

publisherap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/publisher

scope noteap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#scopeNote

A note that helps to clarify the meaning and/or the use of a concept.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
note ap

see also EMBL sequenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefEMBLSequence

This cross-reference relates a given resource to any EMBL sequence database resource.
has super-properties
see Also

see also Ensembl cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefEnsembl

This cross-reference relates a given resource to any Ensembl database resource.
has super-properties
see Also
has sub-properties
see also Ensembl gene ap, see also Ensembl protein ap, see also Ensembl transcript ap

see also Ensembl geneap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefEnsemblGene

This cross-reference relates a given resource to an Ensembl gene. URI RDF instance template to assign this property: http://rdf.ebi.ac.uk/resource/ensembl/{ENSEMBL_GENE_ID}. Example: :ANY_URI lscr:xrefEnsemblGene http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000139618
has super-properties
see also Ensembl cross-reference ap
has range
Gene c

see also Ensembl proteinap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefEnsemblProtein

This cross-reference relates a given resource to an Ensembl protein. URI RDF instance template to assign this property: http://rdf.ebi.ac.uk/resource/ensembl.protein/{ENSEMBL_PROTEIN_ID}. Example: :ANY_URI lscr:xrefEnsemblProtein http://rdf.ebi.ac.uk/resource/ensembl.protein/ENSP00000296370
has super-properties
see also Ensembl cross-reference ap
has range
protein c

see also Ensembl transcriptap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefEnsemblTranscript

This cross-reference relates a given resource to an Ensembl transcript. URI RDF instance template to assign this property: http://rdf.ebi.ac.uk/resource/ensembl.transcript/{ENSEMBL_TRANSCRIPT_ID}. Example: :ANY_URI lscr:xrefEnsemblTranscript http://rdf.ebi.ac.uk/resource/ensembl.transcript/ENST00000380152
has super-properties
see also Ensembl cross-reference ap
has range
Transcript c

see also MBGD cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefMBGD

This cross-reference relates a given resource to any MBGD database resource. MBGD: Microbial Genome Database for Comparative Analysis - mbgd.genome.ad.jp .
has super-properties
see Also
has sub-properties
see also MBGD gene ap, see also MBGD gene group ap

see also MBGD geneap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefMBGDGene

This cross-reference relates a given resource to an MBGD gene. MBGD: Microbial Genome Database for Comparative Analysis - mbgd.genome.ad.jp .
has super-properties
see also MBGD cross-reference ap

see also MBGD gene groupap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefMBGDGroup

This cross-reference relates a given resource to an MBGD group of genes. MBGD: Microbial Genome Database for Comparative Analysis - mbgd.genome.ad.jp .
has super-properties
see also MBGD cross-reference ap

see also NCBI cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefNCBI

This cross-reference relates a given resource to any NCBI database resource. NCBI: National Center for Biotechnology Information - https://www.ncbi.nlm.nih.gov/ .
has super-properties
see Also
has sub-properties
see also NCBI RefSeq ap, see also NCBI gene ap, see also NCBI protein ap

see also NCBI geneap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefNCBIGene

This cross-reference relates a given resource to an NCBI gene resource. NCBI: National Center for Biotechnology Information - https://www.ncbi.nlm.nih.gov/ .
has super-properties
see also NCBI cross-reference ap

see also NCBI proteinap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefNCBIProtein

This cross-reference relates a given resource to an NCBI protein resource. NCBI: National Center for Biotechnology Information - https://www.ncbi.nlm.nih.gov/ .
has super-properties
see also NCBI cross-reference ap

see also NCBI RefSeqap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefNCBIRefSeq

This cross-reference relates a given resource to an NCBI Reference Sequence Database (RefSeq) resource. NCBI: National Center for Biotechnology Information - https://www.ncbi.nlm.nih.gov/ .
has super-properties
see also NCBI cross-reference ap

see also OMA cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefOMA

This cross-reference relates a given resource to an OMA database resource.
has super-properties
see Also
has sub-properties
see also OMA group ap, see also OMA protein ap

see also OMA groupap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefOMAGroup

This cross-reference relates a given resource to an OMA group of sequences (e.g.: proteins).

see also OMA proteinap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefOMAProtein

This cross-reference relates a given resource to an OMA proteins. URI RDF instance template to assign this property: http://omabrowser.org/ontology/oma#PROTEIN_{OMA_ID}. Example: :ANY_URI lscr:xrefOMAProtein http://omabrowser.org/ontology/oma#PROTEIN_HUMAN22168
has super-properties
see also OMA cross-reference ap
has range
Protein c

see also UniProt cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefUniprot

This cross-reference relates a given resource to a UniProt protein. URI RDF instance template to assign this property: http://purl.uniprot.org/uniprot/{UNIPROT_ID}. Example: :ANY_URI lscr:xrefUniprot http://purl.uniprot.org/uniprot/P68871
has super-properties
see Also
has sub-properties
see also UniProt/SwissProt cross-reference ap, see also UniProt/TrEMBL cross-reference ap
has range
Protein c

see also UniProt/SwissProt cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefSwissProt

This cross-reference relates a given resource to a UniProt/SwissProt protein. URI RDF instance template to assign this property: http://purl.uniprot.org/uniprot/{UNIPROT_ID}. Example: :ANY_URI lscr:xrefSwissProt http://purl.uniprot.org/uniprot/P68871
has super-properties
see also UniProt cross-reference ap
has range
Protein c

see also UniProt/TrEMBL cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefTrEMBL

This cross-reference relates a given resource to a UniProt/TrEMBL protein. URI RDF instance template to assign this property: http://purl.uniprot.org/uniprot/{UNIPROT_ID}. Example: :ANY_URI lscr:xrefTrEMBL http://purl.uniprot.org/uniprot/H3BS01
has super-properties
see also UniProt cross-reference ap
has range
Protein c

source definitionap back to ToC or Annotation Property ToC

IRI: http://www.ebi.ac.uk/efo/source_definition

statusap back to ToC or Annotation Property ToC

IRI: http://purl.org/ontology/bibo/status

titleap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/title

Named Individuals

average expressedni back to ToC or Named Individual ToC

IRI: http://purl.org/genex#AVERAGE_EXPRESSED

high confidence levelni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/CIO_0000029

A confidence level representing a high trust in an evidence.
Is defined by
http://purl.obolibrary.org/obo/cio.owl

high expressedni back to ToC or Named Individual ToC

IRI: http://purl.org/genex#HIGH_EXPRESSED

highly expressedni back to ToC or Named Individual ToC

IRI: http://purl.org/genex#HIGHLY_EXPRESSED

g is highly expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background i.e all gene expressions taking into account a given gene expression condition.

https://www.sib.swissni back to ToC or Named Individual ToC

IRI: https://www.sib.swiss

belongs to
Organization c
has facts
homepage ap "https://www.sib.swiss"
name ap "SIB Swiss Institute of Bioinformatics"@en

https://www.unil.chni back to ToC or Named Individual ToC

IRI: https://www.unil.ch

belongs to
Organization c
has facts
homepage ap "https://www.unil.ch"
name ap "University of Lausanne"@en

low confidence levelni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/CIO_0000031

A confidence level representing an absence of trust in an evidence.
Is defined by
http://purl.obolibrary.org/obo/cio.owl

low expressedni back to ToC or Named Individual ToC

IRI: http://purl.org/genex#LOW_EXPRESSED

lowly expressedni back to ToC or Named Individual ToC

IRI: http://purl.org/genex#LOWLY_EXPRESSED

g is lowly expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.

medium confidence levelni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/CIO_0000030

A confidence level representing a moderate trust in an evidence.
Is defined by
http://purl.obolibrary.org/obo/cio.owl

Taxonomic rank Speciesni back to ToC or Named Individual ToC

IRI: http://purl.uniprot.org/core/Species

belongs to
Taxon rank c

ubiquitously expressedni back to ToC or Named Individual ToC

IRI: http://purl.org/genex#UBIQUITOUSLY_EXPRESSED

x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x.

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals
ep: External Properties